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The anti-theft PATS system is mainly controlled by the instrument cluster. This is where the Key info is stored. Since you haven't changed the cluster, there is no need to reprogram the keys. The Instrument cluster and the ECM are a matched pair and that is why your's will not start. You will need to perform a "parameter reset" to resync up your new ECM to your Cluster. It looks like you will need a NGS tester or equivalent (Dealer) to do this.
couldn't he just reprogram the key to the new ECM like it says in the instruction manual about programming new keys?
~Matt
No, the keys are programmed into the Instrument Cluster, not the ECM. His problem is that the Cluster and ECM are not "getting along". They do this to make it more difficult to steal.